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SNP FAQ Archive [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2005-.

  • This publication is provided for historical reference only and the information may be out of date.

This publication is provided for historical reference only and the information may be out of date.

Submission Errors and Submission Withdrawal

Created: ; Last Update: June 15, 2010.

Estimated reading time: 2 minutes

Withdrawing Data from dbSNP

Is it possible to withdraw submissions from dbSNP?

Yes, a submitter may withdraw a submission from dbSNP by formatting the withdrawals in the format defined in the dbSNP submission documentation and sending them to dbSNP at vog.hin.mln.ibcn@etadpu-pns. Please note, however, that it is not possible to completely eliminate a withdrawn record from the database since a submission quickly becomes permanently associated with dbSNP records and records in other databases. The withdrawn record will retain its original submitted SNP (ss) ID number, but the SNP will be removed from the “SNP” table and placed in the “delete history” table. If you search for a ss ID number that has been withdrawn, you will get a report that describes the submission and withdrawal data. (01/31/08)

Fixing Errors in Submitted Data

I submitted some SNPs to you last week, but just now found an error in the sequence data for one of my submissions. What should I do?

Send the correct sequence for this submission, and we will update the existing record. (4/21/06)

We would like to resubmit SNP data that we have revised from an earlier submission. Do we withdraw our previously submitted batches of SNPs?

dbSNP can either withdraw the batches or you can do a resubmission, and we'll update and replace the previous batches. Please send the updates to vog.hin.mln.ibcn@etadpu-pns.

Renaming SNPs

Sequences for several loci that we have submitted to dbSNP don't BLAST back to Genbank records for the same gene. We renamed the SNPs in our publication so that they would not be associated with the gene, but how do we do this for the data we submitted to dbSNP?

Send dbSNP a list of the submitted SNP numbers (ss#) for the data you submitted, the old names for the SNPs, the new names for the SNPs, to vog.hin.mln.ibcn@setadpu-pns ; we'll revise your records, and remove the association with the gene.(9/19/06)

Why Specific RefSNPs have been withdrawn/deleted from dbSNP

Why has rs11568324 been deleted from dbSNP? We, and other groups have genotyped this SNP, and although the minor allele frequency is very low (0.7%), we consistently found this SNP.

The rs11568324 cluster contained two submitted SNPs (ss#), both of which were from the same submitter. This submitter also submitted a “withdraw” request on September 7, 2006 for the SNPs in question.

The submitter has since re-analyzed their SNP data and has resubmitted their SNPs to us. The submitter indicated that their newly submitted SNPs may include some previously withdrawn SNPs. We are in the process of mapping the new SNPs from this submitter, and if any of these SNPs map to the position that rs11568324 used to map to, they will be assigned to that cluster.(11/21/06)

I searched db SNP several months ago for SNPs in SLC22A2 and its splicing variations, and found non- synonymous SNPs. I searched again today, and found that many of these SNPs have been deleted from dbSNP. Why?

The SNPs mentioned in your question were originally submitted by PHARMGKB (to see the submitter of a ss#, click on the ss#, which is located in the “NCBI Assay ID” column of the “Submitter Records” section of the refSNP report page). PHARMGKB has withdrawn 11740 of their submitted SNPs (ss#) for error corrections and will resubmit the data early next year (2007). PHARMGKB did not indicate the percentage of corrected SNPs that will have flanking sequence changes. (12/19/06)

Why was rs2228570 withdrawn form dbSNP? I can’t find it using Entrez SNP.

rs2228570 has not been withdrawn from dbSNP; however, it does not map to the genome assemblies, which may be due to the fact that this SNP was derived from cDNA. Since rs2228570 does not map to the genome assemblies, you won’t see it in Entrez SNP. I can tell you that rs2228570 is located in NM_000376. Future releases of Entrez SNP will include all SNPs —those that map to genome assemblies, and those that don’t. (2/16/07)

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